The identification result of MAP-Match and conventional method
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ABSTRACT: The comparison of GPSMs that's identified by StrucGP in 24 MouseBrain raw files, using MAP-Match and the conventional calibration method saparately.
Project description:In this study, we applied the recently developed software, StrucGP to large-scale characterize glycoproteins, and IGPs, as well as precise site-specific glycan structures in human spermatozoa. Furthermore, bioinformatical analyses were conducted to systematically describe the potential functions of N-glycosylation in human spermatozoa.
Project description:In this project we developed a new algorithm termed StrucGP, for large-scale interpretation of N-glycan structures on intact glycopeptides from tandem mass spectrometry data. StrucGP is able to reveal the glycan structure heterogeneity for individual glycosites. The StrucGP also has high performance in distinguishing various structure isoforms and identifying new and rare glycan structures from complex samples.
Project description:Spike (S) protein plays a key role in COVID-19 (SARS-CoV-2) infection and host-cell entry. Previous studies have systematically analyzed site-specific glycans compositions of S protein. Here, we further provide structure-clear N-glycosylation of S protein at site-specific level by using our recently developed structure- and site-specific N-glycoproteomics sequencing algorithm StrucGP. In addition to the common N-glycans as detected in previous studies, many uncommon glycosylation structures such as LacdiNAc structures, Lewis structures, Mannose 6-Phosphate (M6P) residues and bisected core structures were unambiguously mapped at a total of 20 glycosites in the S protein trimer and protomer. These data further supports the glycosylation structural-functional investigations of COVID-19 virus Spike.
Project description:Full title: Three-dimensional culture of AIDS-NHL cells influences gene expression related to B-cell development, proliferation and survival The AIDS-NHL-derived cell line, UMCL01-101, representing diffuse large B-cell lymphoma of immunoblastic morphology (AIDS-IBL), was grown in conventional, static suspension culture or three-dimensionally (3D) in the Rotating Wall Vessel (RWV) bioreactor. The objective was to assess the impact on gene expression of growth as a three-dimensional tissue assembly. Global gene expression analysis was performed on UMCL01-101 cells grown under either condition using Affymetrix microarray. UMCL01-101 cells were cultured in the Rotating Wall Vessel bioreactor to form 3D assemblies, or in conventional suspension culture, for 15 days. RNA was prepared from triplicate samples under each growth condition and submitted for microarray analysis.
Project description:In this study, we used human THP-1-derived macrophages as an immune cell model, and systematically performed glycoproteomics of three subtypes of macrophages by StrucGP.To study the N‑Glycoproteomic of them, the intact glycopeptides were first enriched and identified using triplicate mass spectrometry (MS)-based glycoproteomic approaches, then StrucGP was used for subsequent analysis. In total three subtypes of macrophages, these intact glycopeptides consist of 253 N-linked glycan structures at 652 unique glycosites from 372 N-glycoproteins, along with their PSM information. A total of 135, 163, and 201 N-glycan structures were identified from M0, M1, and M2 macrophages, respectively.
Project description:High resolution Mass Spectrometry and Peptides identification uncovered ancestral giant insect viruses motifs within Histone-4 peptides in human liver cells. These peptides did not match any human sequence. This finding consolidates the dogma that molecular patterns are universal and suggests that metazoan cellular structures possibly share an evolutionary link with ancient giant viruses.
Project description:Data independent acquistion (DIA) is becoming widely as a method of choice in quantitation proteomics due to its high reproducibility and quantitation accuracy at high-throughput fashion. In this project, we systematically evaluated the effect of the selected precursor mass range for DIA-MS on the protein identification and quantification. We show that a narrow precursor window (400-650 m/z) DIA could identify a 34.7% more proteins than a conventional DIA with a wide precursor window of 400-1200 m/z. When combining the three narrow precursor windows (400-650, 650-900, and 900-1200 m/z) DIA-MS analyses, we obtained a 59.4% increase in the number of proteins quantified than a conventional DIA-MS analysis.
Project description:PAM50 intrinsic subtype classification (Parker JS, Mullins M, Cheang MCU, et al: Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes. J Clin Oncol 27:1160-1167, 2009) was used for the Z1031 patient cohort. However, to account for potential technical biases such as differences in platforms and laboratory protocols between the Z1031 data set and the PAM50 training set2, we normalized the Z1301 data set before applying the PAM50 algorithm. This is a critical step that must be taken into consideration for appropriate subtype predictions as our group and others have previously shown3,4. To appropriately normalize the Z1301 microarray data, which is entirely composed of ER-positive tumors, we needed to estimate technical bias from a cohort with equivalent subtype representation as the PAM50 training set. A set including ER-negative, HER2-positive and true normal breast samples were profiled under the same platform, protocol and laboratory (i.e. WashU) as the Z1301 data set. A total of 40 prototypic samples of the various molecular subtypes were selected to match the distribution in the PAM50 training set. The mean expression of each PAM50 gene was calculated in this set of 40. These values obtained from the prototypical sample set were used for calibration purposes and were included as a new WashU_4X44K_Calibration column in the CalibrationParameter file, which has been already provided in the PAM50 algorithm2. This adjustment step assures that each sample is placed in the appropriate ‘prototypic space’ by subtracting the calibration value of each PAM50 gene from the expression value of the corresponding gene in each tested sample. Finally, single sample predictions were performed in every Z1301 sample using the WashU_4X44K_Calibration parameter. The complete data set for the 40 prototypic arrays is submitted under GSE26082. 40 experiments were used as prototypical cases for subtype calibration purposes.
Project description:In this dataset, we investigate the targets of degrasyn in the methicillin-sensitive S. aureus strain NCTC 8325. This includes data on enrichment studies and competition studies with conventional ABPP using a degrasyn-derived probe, competition studies with residue-specific proteomics using the isoDTB-ABPP method and global analysis of protein expression levels in response to degrasyn treatment.